Mercurial > repos > bgruening > agat

comparison test-data/functional_annot/report.txt @ 3:a6318f87f2cd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
author bgruening
date Thu, 15 Feb 2024 15:47:19 +0000
parents
children e7449b2c14bf
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2:e009d8260be2 3:a6318f87f2cd
1 02/15/2024
2 usage: /home/rlibouba/miniconda3/envs/__agat@1.2.0/bin/agat_sp_manage_functional_annotation.pl --gff annotation.gff -i /tmp/tmpvotn3s2b/files/d/a/b/dataset_dab3424c-9f01-4319-a841-302674d17b7c.dat -pe 5 -o galaxy_functional_annot
3 --------------------------------------------------------------------------------
4
5 ------------------------------------- mrna -------------------------------------
6 Number of gene 2
7 Number of mrna 2
8 Number of cds 2
9 Number of exon 2
10 Number of exon in cds 2
11 Number gene overlapping 0
12 Number of single exon gene 2
13 Number of single exon mrna 2
14 mean mrnas per gene 1.0
15 mean cdss per mrna 1.0
16 mean exons per mrna 1.0
17 mean exons per cds 1.0
18 Total gene length (bp) 3294
19 Total mrna length (bp) 3294
20 Total cds length (bp) 3294
21 Total exon length (bp) 3294
22 mean gene length (bp) 1647
23 mean mrna length (bp) 1647
24 mean cds length (bp) 1647
25 mean exon length (bp) 1647
26 mean cds piece length (bp) 1647
27 Longest gene (bp) 2415
28 Longest mrna (bp) 2415
29 Longest cds (bp) 2415
30 Longest exon (bp) 2415
31 Longest cds piece (bp) 2415
32 Shortest gene (bp) 879
33 Shortest mrna (bp) 879
34 Shortest cds piece (bp) 879
35
36 ---------------------------------- transcript ----------------------------------
37 Number of gene 8
38 Number of transcript 8
39 Number of cds 7
40 Number of exon 8
41 Number of exon in cds 7
42 Number gene overlapping 2
43 Number of single exon gene 8
44 Number of single exon transcript 8
45 mean transcripts per gene 1.0
46 mean cdss per transcript 0.9
47 mean exons per transcript 1.0
48 mean exons per cds 1.0
49 Total gene length (bp) 6501
50 Total transcript length (bp) 6501
51 Total cds length (bp) 5688
52 Total exon length (bp) 6501
53 mean gene length (bp) 812
54 mean transcript length (bp) 812
55 mean cds length (bp) 812
56 mean exon length (bp) 812
57 mean cds piece length (bp) 812
58 Longest gene (bp) 1149
59 Longest transcript (bp) 1149
60 Longest cds (bp) 1149
61 Longest exon (bp) 1149
62 Longest cds piece (bp) 1149
63 Shortest gene (bp) 399
64 Shortest transcript (bp) 399
65 Shortest cds piece (bp) 399
66
67 _________________________________________________________________________________________________________________________________
68 | | Nb Total term | Nb mRNA with term | Nb mRNA updated by term | Nb gene updated by term |
69 | | in raw File | in raw File | in our annotation file | in our annotation file |
70 |_________________________________________________________________________________________________________________________________|
71 | GO | 1 | | 0 | 0 |
72 |_________________________________________________________________________________________________________________________________|
73 | InterPro | 2 | | 0 | 0 |
74 |_________________________________________________________________________________________________________________________________|
75 | MetaCyc | 275 | | 0 | 0 |
76 |_________________________________________________________________________________________________________________________________|
77 | ProSitePatterns | 2 | | 0 | 0 |
78 |_________________________________________________________________________________________________________________________________|
79 | Reactome | 95 | | 0 | 0 |
80 |_________________________________________________________________________________________________________________________________|
81
82 nb mRNA without Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 10
83 nb mRNA with Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 0
84 nb gene without Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 10
85 nb gene with Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 0